3DZA | pdb_00003dza

Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DZA/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-29 Released: 2008-08-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.152 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative membrane protein of unknown function (YP_001337144.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.65 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 83.64 kDa
Atom Count: 6,799
Modelled Residue Count: 711
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized putative membrane protein	A, B, C, D	191	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: YP_001337144.1, yfdX, KPN78578_34530, KPN_03482
UniProt
Find proteins for A6TE93 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TE93 Go to UniProtKB: A6TE93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TE93
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] E [auth A] F [auth A] G [auth A] GA [auth D] AA [auth C], E [auth A], F [auth A], G [auth A], GA [auth D], M [auth B], N [auth B], X [auth C], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain Q [auth B] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] H [auth A] CA [auth C], DA [auth C], EA [auth C], FA [auth C], H [auth A], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], Q [auth B], QA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	BA [auth C], HA [auth D], IA [auth D], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.194 (Depositor), 0.200 (DCC)
R-Value Work: 0.152 (Depositor), 0.160 (DCC)
R-Value Observed: 0.154 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33DZA

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.207	α = 90
b = 79.016	β = 90
c = 137.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Refinement description, Structure summary